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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Methods for safely sharing dual-use genetic data

Background: Some genetic data has dual-use potential. Sharing pathogen data has shown tremendous value. For example therapeutic development and lineage tracking during the COVID pandemic. This data sharing is complicated by the fact that these data have the potential to be used for harm. The genome sequence of a pathogen can be used to enable malicious genetic engineering approaches or to recreate the pathogen from synthetic DNA. Standard data security methods can be applied to genetic data, but when data is shared between institutions, ensuring appropriate security can be difficult. Sensitive data that is shared internationally among a wide array of institutions can be especially difficult to control. Methods for securely storing and sharing genetic data with potential for dual-use are needed to mitigate this potential harm.Results: Here we propose new methods that allow genetic data to be shared in a data format that prevents a nefarious actor from accessing sensitive aspects of the data. Our methods obfuscate raw sequence data by pooling reads from different samples. This approach can ensure that data is secure while stored and during electronic transfer. We demonstrate that by pooling raw sequence data from multiple samples of the same organism, the ability to fully reconstruct any individual sample is prevented. In the pooled data, most genomic information remains, but reads or mutations cannot be directly attributed to any individual sample. To further restrict access to information, regions of a genome can be removed from the reads.Conclusion: Our methods obscure genomic information within raw sequence reads. This method can allow genetic data to be stored and shared while preventing a nefarious actor from being able to perfectly reconstruct an organism. Broad-scale sequence information remains, while fine scale details about specific samples are difficult or impossible to reconstruct. Our software is available at https://github.com/Geneinfosec-Inc/ReadMixer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Applied genomics for industrially relevant microalgal strain development & optimization: characterizing genotype-phenotype relationships towards scalable environment-enhancing energy systems

Multiple planetary boundaries considered a safe operating space for humanity have been exceeded in recent years, with twice as many boundaries transgressed in 2023 as in 2009. Bioenergy systems are unique in that they can interact with and improve many of the transgressed boundaries directly, including multiple geochemical cycles, water and land use, and climate change. Among bioenergy systems, microalgae-based environment enhancing energy (E 2 -energy) are promising bioenergy systems for drop-in biofuels, valuable materials, chemicals and therapeutics, while making deep emission cuts and remediating wastewater, all without competing for agricultural resources.

09 BIOMASS FUELS↗
DOE OSTI2025

From quantitative trait loci towards mechanisms: Linkage Integration Hypothesis Testing (LIgHT) sheds light on the mechanisms of genetically modulated stress tolerance

The goal of this work is to assess the mechanistic bases of natural genetic variations in plant responses of photosynthesis to stress. To achieve this goal, we devised the Linkage Integration Hypothesis Testing (LIgHT) approach, comparing chromosomal locations of quantitative trait loci (QTLs) for multiple phenotypes to distinguish between hypothetical mechanisms. As a use case, we explored genetic variations in photosynthesis-related processes under chilling stress in recombinant inbred lines of cowpea ( Vigna unguiculata L. Walp.). We focused on photosynthesis-related parameters measurable in high throughput and indicative of proposed chilling responses, including the states of PSI and PSII, photoprotective non-photochemical quenching, PSII photodamage, and nyctinastic leaf movements (NLMs). The patterns of QTL linkages indicated that chilling stress tolerance is genetically controlled by avoiding PSII photodamage rather than PSI damage or NLMs. This model was validated in a separate experiment measuring the rates of PSII photodamage and repair. Additional linkages suggest that chilling-induced damage to PSII is controlled by the thylakoid proton motive force and redox state of PSII. This regulation appears to be modulated by thylakoid fatty acid composition, previously associated with the same genetic loci and now supported by broader mechanistic evidence. We propose that the LIgHT approach can be broadly applied to test mechanisms underlying genetic variations.

MultispeQ↗
DOE OSTI2026

Genome_shuffling_enables_quantitative_trait_locus_mapping_in_Bacillus_subtilis

Genetic mapping is a powerful tool for eukaryotic genetics that has only been applied to bacteria in limited circumstances. Quantitative trait locus (QTL) mapping generally relies on sexual recombination to break linkages between genes, yet bacteria rarely undergo sufficient homologous recombination to generate suitable mapping populations. In this work, we used iterative biparental genome shuffling by protoplast fusion inBacillus subtilisto generate a population of bacteria with substantial random recombination throughout their genomes. Individual shuffled progeny were arrayed in well plates, resequenced, and characterized for a range of complex phenotypes including spore germination and swarming motility. Genetic mapping of the resulting phenotypes identified high-confidence QTLs of moderate size (∼10 kb), and these associations were validated through targeted genetic swaps. ThisB. subtilisQTL population can easily be used to map additional phenotypes, and the general approach for QTL mapping is applicable in a wide range of bacteria.

Bacillus subtilis↗
DOE OSTI2026

Genome shuffling enables quantitative trait locus mapping in Bacillus subtilis

Genetic mapping is a powerful tool for eukaryotic genetics that has only been applied to bacteria in limited circumstances. Quantitative trait locus (QTL) mapping generally relies on sexual recombination to break linkages between genes, yet bacteria rarely undergo sufficient homologous recombination to generate suitable mapping populations. In this work, we used iterative biparental genome shuffling by protoplast fusion in Bacillus subtilis to generate a population of bacteria with substantial random recombination throughout their genomes. Individual shuffled progeny were arrayed in well plates, resequenced, and characterized for a range of complex phenotypes including spore germination and swarming motility. Genetic mapping of the resulting phenotypes identified high-confidence QTLs of moderate size (~10 kb), and these associations were validated through targeted genetic swaps. This B. subtilis QTL population can easily be used to map additional phenotypes, and the general approach for QTL mapping is applicable in a wide range of bacteria.

Vasileva, Delyana [ORNL] (ORCID:0000000279197883)↗
DOE OSTI2026

Optimizing pressurized-water reactor equilibrium cycle using a novel loading pattern encoding and rule-based genetic crossover operators

This work presents an extended multi-batch approach applied in shuffling scheme optimization for equilibrium cycle for pressurized water reactors using Genetic Algorithms (GAs). A new ruled based GA crossover operator called Inherited Location and Batch (ILB) was introduced to enhance offsprings reproduction efficiency specialized for equilibrium cycle optimization problem. This approach was implemented within the Plant ReLoad Optimization (PRLO) framework and validated using a generic reactor model based on the AP1000 design, with core parameters calculated via the CASMO/SIMULATE software package. The ILB approach is then applied for both single and multi-objective problems in maximizing cycle length and core average exposure while minimizing the average enrichment of the 57 fresh fuel assemblies (FAs) per cycle. The optimal solutions are selected based on their dominance to the objectives from all feasible solutions. This research identified three optimal solutions satisfied safety constraints: The first solution minimizes feed enrichment costs with a cycle length of 338.8 days and core exposure of 25.39 MWd/MT; the second solution extends cycle length to 361.2 days, with the highest core exposure of 26.84 MWd/MT, using 3.75 wt% average fuel enrichment; the third solution balances both objectives with a cycle length of 349.6 days, core exposure of 25.82 MWd/MT with a slight enrichment increase compared to the first solution. Collectively, these findings underscore the efficiency and effectiveness of the proposed approach in achieving practical multi-objective optimal equilibrium cycle designs using GAs optimizer.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2024

Omics-driven onboarding of the carotenoid producing red yeast Xanthophyllomyces dendrorhous CBS 6938

Transcriptomics is a powerful approach for functional genomics and systems biology, yet it can also be used for genetic part discovery. Here, we derive constitutive and light-regulated promoters directly from transcriptomics data of the basidiomycete red yeast Xanthophyllomyces dendrorhous CBS 6938 (anamorph Phaffia rhodozyma) and use these promoters with other genetic elements to create a modular synthetic biology parts collection for this organism. X. dendrorhous is currently the sole biotechnologically relevant yeast in the Tremellomycete class-it produces large amounts of astaxanthin, especially under oxidative stress and exposure to light. Thus, we performed transcriptomics on X. dendrorhous under different wavelengths of light (red, green, blue, and ultraviolet) and oxidative stress. Differential gene expression analysis (DGE) revealed that terpenoid biosynthesis was primarily upregulated by light through crtI, while oxidative stress upregulated several genes in the pathway. Further gene ontology (GO) analysis revealed a complex survival response to ultraviolet (UV) where X. dendrorhous upregulates aromatic amino acid and tetraterpenoid biosynthesis and downregulates central carbon metabolism and respiration. The DGE data was also used to identify 26 constitutive and regulated genes, and then, putative promoters for each of the 26 genes were derived from the genome. Simultaneously, a modular cloning system for X. dendrorhous was developed, including integration sites, terminators, selection markers, and reporters. Each of the 26 putative promoters were integrated into the genome and characterized by luciferase assay in the dark and under UV light. The putative constitutive promoters were constitutive in the synthetic genetic context, but so were many of the putative regulated promoters. Notably, one putative promoter, derived from a hypothetical gene, showed ninefold activation upon UV exposure. Thus, this study reveals metabolic pathway regulation and develops a genetic parts collection for X. dendrorhous from transcriptomic data. Therefore, this study demonstrates that combining systems biology and synthetic biology into an omics-to-parts workflow can simultaneously provide useful biological insight and genetic tools for nonconventional microbes, particularly those without a related model organism. This approach can enhance current efforts to engineer diverse microbes.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1985

Report of the Microbial Development Working Group

In formulating ideas on the relationship of gravity to the development, growth, and reproduction of microorganisms, a rather liberal definition of microorganisms is used which includes bacteria, yeasts, protists, filamentous fungi, and single cells in culture. A principal advantage of microorganisms as experimental subjects is the rigor with which they can be defined and controlled. As single cells, each cell may be regarded as identical to the others in the population. This property applies to the morphology, physiology, and genetic parameters of the cells. The growth and development of the population is subject to precise manipulation as the nutritional requirements are known and minimal media formulations have been developed. Growth and differentiation can be manipulated in a variety of ways, such as alteration of the culture temperature and food supply, or by use of mutants. Finally, the short generation times of microorganisms provide the opportunity to conduct multigenerational studies within practical time limits and, in a similar vein, cellular responses to various stimuli or stresses are conveniently monitored because of the rapid response times of single cells.

G Nelson↗
DOE OSTI2025

TRACKING LIGNOCELLULOSIC BREAKDOWN BY ANAEROBIC FUNGI AND FUNGAL CELLULOSOMES

Anaerobic fungi degrade plant biomass through invasive, filamentous growth, and the secretion of multi-protein biomass-degrading complexes called fungal cellulosomes. This project developed new tools for anaerobic, non-destructive, real-time imaging of cellulosomes across spatial and temporal scales. Novel nanobody tools were synthesized and deployed to image native fungal cellulosomes. Antibodies raised against key fungal cellulosome components were also used to define the localization patterns of cellulosomes in mature fungal mats vs. fungal zoospores, and revealed direct connections between cellular life stage progression and the regulation of cellulosome production. New procedures were developed to purify native cellulosomes and study their morphology and sub-structures, and genetic engineering tools were also developed and applied to anaerobic fungi to advance in vivo labeling capabilities. A cryoEM structure of a native fungal cellulosome was achieved, as well as a proof of concept for transformation of fungi with flavin-based anaerobic reporter proteins for in vivo labeling of cellulosome components.

09 BIOMASS FUELS↗
DOE OSTI2026

Optimized Gear Selection to Maximize Energy Savings in Electric Traction Drives for Medium and Heavy Duty Vehicles

Multi‑gear transmission systems are commonly used in electric traction drives for medium and heavy‑duty vehicles, while most passenger‑vehicle electric drivetrains rely on a single fixed ratio to reduce cost, weight, and complexity. Using multiple gear ratios can enable downsizing of the motor and inverter while still meeting performance requirements. Additionally, appropriately chosen ratios allow the motor to operate more frequently in high‑efficiency regions, improving overall energy usage and reducing operating costs over the drive cycle. This paper presents a systematic approach for selecting optimal gear ratios for electric drive systems. A neural‑network model is first developed to represent motor losses across the full torque–speed range using data generated from finite element analysis. This model enables fast, accurate evaluation of motor efficiency under varying operating conditions. A genetic‑algorithm‑based optimization framework is then applied to identify gear ratios that maximize energy cost savings over the drive cycle, with the resulting optimal ratios stored for real‑time implementation.

Gadiyar, Nishanth [ORNL] (ORCID:0000000348267524)↗
DOE OSTI2025

OzMALDI: A Gas-Phase, In-Source Ozonolysis Reaction for Efficient Double-Bond Assignment in Mass Spectrometry Imaging with Matrix-Assisted Laser Desorption/Ionization

Lipids make up an important class of biomolecules with diverse structures and varied chemical functions. This diversity is a major challenge in chemical analysis and limits our understanding of biological functions and regulation. A major way lipid isomers differ is by double-bond (db) position, and analyzing db-isomers is especially challenging for mass spectrometry imaging (MSI). Ozonolysis can be used to determine the dbposition and has been paired with MSI before. However, previous techniques require increased analysis time to allow for gas-phase reactions within an ion trap or ion mobility cell or additional sample preparation time to allow for offline ozonation. Here, we introduce a new ozonolysis method inside the matrix-assisted laser desorption-ionization (MALDI) source, termed OzMALDI, that simultaneously produces ozonides from all unsaturated lipids. This allows us to determine db-positions without adding additional reaction time while maintaining the high mass resolution provided by Orbitrap MS. This new technique is especially effective at determining multiple db-positions in lipids containing polyunsaturated fatty acids, which is a limitation of many previous techniques. OzMALDI-MSI was applied to the analysis of rat brain and genetically engineered Camelina and soybean seed samples, demonstrating the utility of this method and uncovering novel biological information.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

A Route to Design Novel Functional Peptides by Applying a Denoising Diffusional Model to mRNA Display Libraries

In vitro directed evolution techniques, such as mRNA display, enable peptide ligand discovery and optimization. However, physical libraries that rely on a genetic code can only search a small fraction of sequence space due to inherent biases in the genetic code and experimental limitations. To address this challenge, denoising diffusion implicit models (DDIMs) are applied to generate novel peptide ligands against B‐cell lymphoma extra‐large (Bcl‐x L ), a key cancer target. Starting with high‐throughput sequencing data from previous selections, a DDIM is trained to produce novel sequences with high affinity binding. Experimental validation confirms that most generated sequences are functionally equivalent to the original library members for Bcl‐x L binding and demonstrated comparable binding kinetics and affinity relative to the wildtype and nearest original neighbors. Importantly, this approach generated rare sequences not easily accessible via mutation and directed evolution. These results indicate that DDIMs can complement and expand directed evolution data, efficiently exploring underrepresented regions of sequence space. This approach provides a broadly applicable framework for accelerating ligand discovery and optimizing molecular properties across diverse targets.

Qi, Pearl [Mork Family Department of Chemical Engi↗
DOE OSTI2026

SAIGE-GPU: accelerating genome- and phenome-wide association studies using GPUs

Genome-wide association studies (GWAS) at biobank scale are computationally intensive, especially for admixed populations requiring robust statistical models. SAIGE is a widely used method for generalized linear mixed-model GWAS but is limited by its CPU-based implementation, making phenome-wide association studies impractical for many research groups. We developed SAIGE-GPU, a GPU-accelerated version of SAIGE that replaces CPU-intensive matrix operations with GPU-optimized kernels. The core innovation is distributing genetic relationship matrix calculations across GPUs and communication layers. Applied to 2068 phenotypes from 635 969 participants in the Million Veteran Program, including diverse and admixed populations, SAIGE-GPU achieved a 5-fold speedup in mixed model fitting on supercomputing infrastructure and cloud platforms. We further optimized the variant association testing step through multi-core and multi-trait parallelization. Deployed on Google Cloud Platform and Azure, the method provided substantial cost and time savings. Source code and binaries are available for download at https://github.com/saigegit/SAIGE/tree/SAIGE-GPU-1.3.3. A code snapshot is archived at Zenodo for reproducibility (DOI: [10.5281/zenodo.17642591]). SAIGE-GPU is available in a containerized format for use across HPC and cloud environments and is implemented in R/C++ and runs on Linux systems.

Rodriguez, Alex [Argonne National Laboratory (ANL)↗
DOE OSTI2025

Synthetic feed-forward loop circuit boosts transgene expression in sugarcane

Bio-based products derived from natural plant-derived materials offer a promising alternative to petroleum-based products, which are essential for achieving global sustainability (Gupta et al. 2022). Sugarcane provides 40% of the world’s biofuel (Brant et al. 2025). Recently, metabolic engineering of sugarcane for hyperaccumulation of biomass oil is emerging as a strategy to elevate the crop’s energy content (Cao et al. 2023; Maitra et al. 2024). Synthetic transcription factors offer a powerful tool for modulating entire metabolic pathways by enabling fine-tuned activation or repression of specific genes (Liu and Stewart 2016; Hooghvorst and Altpeter 2023). However, the application of these technologies faces challenges, including the availability of well-characterized genetic building blocks for precise manipulation of gene expression, and the inherently challenging properties of gene expression in highly polyploid crops like sugarcane (Liu and Stewart 2016).

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Genetically Controlled Iron Oxide Biomineralization in Encapsulin Nanocompartments for Magnetic Manipulation of a Mammalian Cell Line

Magnetic nanoparticles have proven invaluable for biomechanical investigations due to their ability to exert localized forces. However, cellular delivery of exogenous magnetic agents often results in endosomal entrapment, thereby limiting their utility for manipulating subcellular structures. This study characterizes and exploits fully genetically controlled biomineralization of iron-oxide cores inside encapsulin nanocompartments to enable magnetic-activated cell sorting (MACS) and magnetic cell manipulation. The fraction of MACS-retained cells showed substantial overexpression of encapsulins and exhibited both para- and ferrimagnetic responses with magnetic moments of 10 -15 A m 2 per cell, comparable to standard exogenous labels for MACS. Electron microscopy revealed that MACS-retained cells contained densely packed agglomerates of ≈30 nm iron oxide cores consisting of ultrafine quasicrystalline ordered nuclei within an amorphous matrix of iron, oxygen, and phosphorus. Scanning transmission X-ray microscopy, X-ray absorption spectroscopy, and Raman microspectroscopy confirmed that the iron-oxide species are consistent with ferric oxide (Fe 2 O 3 ). In addition, the encapsulin-overexpressing MACS-retained cells can be manipulated by a magnetic needle and regrown in patterns determined by magnetic gradients. This study demonstrates that the formation of quasicrystalline iron oxide with mixed para/ferrimagnetic behavior in the cytosol of mammalian cells enables magnetic manipulation without the delivery of exogenous agents.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Harnessing Machine Learning for Agnostic Biodetection

The United States’ current list-based approach to biodefense is limited because it considers only known biological agents. Alternatively, developing and adopting a system based on agent-agnostic signatures would enable detection and characterization of both known and novel agents, thereby engendering greater adaptability in the face of an evolving threat landscape. Machine learning (ML) could aid in such a transition, as it can recognize and encode highly complex patterns from multiple input data modalities and has already demonstrated success in many healthcare and defense applications. Functionalizing ML for environmental biodetection requires understanding current technical capabilities. In this article, we provide a systematic review of existing ML platforms and discuss anticipated development efforts needed to achieve effective ML-enabled, agnostic biodetection.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Efficient mutagenesis and genotyping of maize inbreds using biolistics, multiplex CRISPR/Cas9 editing, and Indel-Selective PCR

CRISPR/Cas9 based genome editing has advanced our understanding of a myriad of important biological phenomena. Important challenges to multiplex genome editing in maize include assembly of large complex DNA constructs, few genotypes with efficient transformation systems, and costly/labor-intensive genotyping methods. Here we present an approach for multiplex CRISPR/Cas9 genome editing system that delivers a single compact DNA construct via biolistics to Type I embryogenic calli, followed by a novel efficient genotyping assay to identify desirable editing outcomes. We first demonstrate the creation of heritable mutations at multiple target sites within the same gene. Next, we successfully created individual and stacked mutations for multiple members of a gene family. Genome sequencing found off-target mutations are rare. Multiplex genome editing was achieved for both the highly transformable inbred line H99 and Illinois Low Protein1 (ILP1), a genotype where transformation has not previously been reported. In addition to screening transformation events for deletion alleles by PCR, we also designed PCR assays that selectively amplify deletion or insertion of a single nucleotide, the most common outcome from DNA repair of CRISPR/Cas9 breaks by non-homologous end-joining. The Indel-Selective PCR (IS-PCR) method enabled rapid tracking of multiple edited alleles in progeny populations. The ‘end to end’ pipeline presented here for multiplexed CRISPR/Cas9 mutagenesis can be applied to accelerate maize functional genomics in a broader diversity of genetic backgrounds.

59 BASIC BIOLOGICAL SCIENCES↗